I have a 64 bit Windows Server 2003 with IIS6, on which I would like to run some 32 bit websites as well as a few websites, that should run 64 bit. I know how to configure my 64 bit IIS6 to run 32 bits, but this causes all the application pools to run as 32 bit processes. I would like to mix 32 and 64 bit application pools on the same server. Is this possible ?
No it isn't. You need to upgrade to IIS7 for that.
In IIS6 you can set the enable32BitAppOnWin64 flag to true to enable the entire IIS instance to run 32 bit applications even if the server operating system is 64 bit. In IIS7 you can set this flag per application - which isn't possible in IIS6. This is one way of doing it in IIS7 (can be done through UI and file editing as well):
appcmd apppool set /apppool.name:Cool32bitApplicationPool /enable32BitAppOnWin64:true